I remember when the Animation Editor didn't save your animations. Those were the days. Past tense, of course.

In the script section Compiler, find the following def. Add the green lines and delete the red line.

Code:

def pbCompileAnimations
begin
if $RPGVX # ADD pbanims=load_data("Data/PkmnAnimations.rvdata")else # ADD pbanims=load_data("Data/PkmnAnimations.rxdata") # ADD end # ADD
rescue
pbanims=PBAnimations.new
end
move2anim=[[],[]]
if $RPGVX
anims=load_data("Data/Animations.rvdata")
else
anims=load_data("Data/Animations.rxdata")
end
for anim in anims
next if !anim
found=false
for i in 0...pbanims.length
if pbanims[i] && pbanims[i].id==anim.id
pbanims[i]=pbConvertRPGAnimation(anim)# DELETE
found=true
break
end
end
if !found
pbanims[pbanims.length]=pbConvertRPGAnimation(anim)
end
end

Explanation
There are two animation files: "PkmnAnimations.rxdata" is for animations made with the Animation Editor in Essentials, and "Animations.rxdata" is for animations made within the Database (F9) in RMXP. Whenever the game is recompiled, it recompiles the animations, which involves comparing these two files. The deleted red line gave priority to the Database animations, so any animation made by the Animation Editor is replaced by the Database animation if it exists (even if it's blank). That's the opposite of what we want to happen - AE animations should take priority. Deleting the red line makes that so.

The added green lines let you load the correct animation file for comparison.

I still have a bit of testing with this fix to do, to make sure it's relevant in all situations. Currently even empty animations in the AE animations file still take priority over the corresponding Database animation. I may separate move animations and "other" animations, so the AE is solely for move animations and the Database is solely for "other" animations (grass rustling, exclamation marks, common animations, etc.), with no crossover allowed. If anyone knows anything about animations, I'd love to hear your view on this idea (PM/VM me to avoid cluttering this thread).